Plants are crucial to human health since they provide us with oxygen, food, clothing, and medicines. There is a direct link between plant growth and the microbial community that makes up the plant microbiome, both in the narrow region of soil directly influenced by root secretions (the rhizosphere) and within the root itself (endophytic compartment). The relationship between most endophytes and their host plants is not well understood. Metagenomic analyses attempt to catalog entire microbial communities using high throughput sequencing, and do not rely on being able to culture each microbe. Previous work in the sponsor's laboratory to survey the root microbiome in the model plant Arabidopsis thaliana found that the microbial composition of the endophytic compartment was different from both rhizosphere and bulk soil control. Additionally, this approach uncovered a difference between the endophytic compartment microbial community assembled by wild type roots and the community assembled by cpr5, a mutant plant that over-produces the defense hormone Salicylic Acid (SA). The CPR5 protein is known to play important roles in growth and development, yet the roots of cpr5 mutants are only slightly shorter than control plants making it a perfect candidate to explore the intersection between microbial interactions and growth. This project will use a metatranscriptomics approach to sequence the mRNA of the microbiome in cpr5 and wild type plants in a native soil without the bias of first culturing the members of the community. The interactions between host plants and endophytic microbes will be examined in order to identify the biochemical pathways that change over developmental time and when a defense pathway is activated. In addition, a simplified system will examine the transcription that occurs in a subset of fully sequenced microbes that contribute to plant growth, in culture and in mono- and multiple-association with the root. How organisms regulate their response to environmental cues is a fundamental biological question. Understanding the cross-kingdom communication occurring between plant and microbiome will define the genes and pathways that are involved in development, the establishment and maintenance of mutualistic interactions, and coordinate growth versus immune response decisions. This knowledge is likely to be applicable to the communication in microbial communities in other host plants, and can be used to improve plant yields in an environmentally friendly manner, directly improving human health through reduced pesticide usage and improved nutrition.